Merge pull request easybuilders#18216 from sib-swiss/20230628151838_n…

…ew_pr_RMBlast2140

{bio}[foss/2021a,gompi/2021a] RMBlast v2.14.0, RepeatMasker v4.1.5 w/ Python 3.9.5

easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb

@@ -0,0 +1,63 @@
+##
+# EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <[email protected]>, Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of
+# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'RMBlast'
+version = '2.14.0'
+
+homepage = 'https://www.repeatmasker.org/rmblast/'
+description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary
+ difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn'
+ for use with RepeatMasker and RepeatModeler."""
+
+toolchain = {'name': 'gompi', 'version': '2021a'}
+toolchainopts = {'usempi': True}
+
+# RMBlast is distributed as a patch that applies on top of BLAST+
+source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/']
+sources = ['ncbi-blast-%(version)s+-src.tar.gz']
+patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)]
+checksums = [
+    {'ncbi-blast-2.14.0+-src.tar.gz': 'bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500'},
+    {'isb-2.14.0+-rmblast.patch.gz': '9de0e67467a4cffdde0c5f67e3658fb52ed313e4550f9a36a251bddb2ba33f49'},
+]
+
+dependencies = [
+    ('zlib',          '1.2.11'),
+    ('bzip2',         '1.0.8'),
+    ('PCRE',          '8.44'),
+    ('Boost.MPI',     '1.76.0'),
+    ('GMP',           '6.2.1'),
+    ('libpng',        '1.6.37'),
+    ('libjpeg-turbo', '2.0.6'),
+    ('LMDB',          '0.9.28'),
+]
+
+# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards)
+# Compilation fails on src/algo/blast/api/prelim_stage.cpp
+local_apimake = 'src/algo/blast/api/Makefile.xblast.lib'
+preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake
+
+configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 "
+configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST "
+configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG "
+configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB"
+
+prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && "
+
+sanity_check_paths = {
+    'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2021a.eb

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+easyblock = 'Tarball'
+
+name = 'RepeatMasker'
+version = '4.1.5'
+
+homepage = 'https://www.repeatmasker.org/'
+description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats
+ and low complexity DNA sequences."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+source_urls = ['https://www.repeatmasker.org/%(name)s']
+sources = [
+    SOURCE_TAR_GZ,
+    # optional but recommended: RepBase RepeatMasker Edition
+    # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php
+    # {
+    #     'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz',
+    #     'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1",
+    # },
+]
+checksums = ['16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f']
+
+dependencies = [
+    ('Python',  '3.9.5'),
+    ('Perl',    '5.32.1'),
+    ('TRF',     '4.09.1'),
+    ('h5py',    '3.2.1'),
+    # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match
+    ('HMMER',   '3.3.2'),
+    ('RMBlast', '2.14.0'),
+]
+
+local_default_search_engine = 'RMBlast'
+
+local_config_command = 'cd %(installdir)s &&'
+local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" '
+local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" '
+local_config_command += '-default_search_engine %s' % local_default_search_engine.lower()
+
+postinstallcmds = [local_config_command]
+
+fix_perl_shebang_for = ['RepeatMasker']
+
+sanity_check_paths = {
+    'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'],
+    'dirs': ['Libraries', 'util'],
+}
+
+sanity_check_commands = ['RepeatMasker -help']
+
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': '',
+}
+
+moduleclass = 'bio'